GeneSetCollection-methods {GSEABase} | R Documentation |
Use GeneSetCollection
to construct a collection of gene sets
from GeneSet
arguments, or a list of
GeneSet
s.
GeneSetCollection(object, ..., idType, setType)
object |
An argument determining how the gene set collection will be created, as described in the methods section. |
... |
Additional arugments for gene set collection construction, as described below. |
idType |
An argument of class
GeneIdentifierType , used to
indicate how the geneIds will be represented. |
setType |
An argument of class
CollectionType , used to indicate how the
collection is created. |
signature(object = "GeneSet",idType="missing", setType="missing")
GeneSet
arugments.
signature(object = "list", idType="missing", setType="missing")
GeneSet
s.
signature(object="missing", idType="AnnotationIdentifier", setType="CollectionType")
,
signature(object="missing", idType="AnnotationIdentifier", setType="CollectionIdType")
CollectionType
entities (e.g., pathways for
KEGGCollection
, protein families for PfamCollection
)
implied by the map found in annotation(idType)
. If setType
is a
CollectionIdType
and length(ids(setType))>0
, the
gene set collection is filtered to contain only those sets implied
by the ids.
signature(object="character", idType="AnnotationIdentifier", setType="CollectionType")
,
signature(object="character", idType="AnnotationIdentifier", setType="CollectionIdType")
CollectionType
entities (e.g., pathways for
KEGGCollection
, protein families for PfamCollection
)
implied by the map found in annotation(idType)
. Use only
those identifiers in object
. If setType
is a
CollectionIdType
and length(ids(setType))>0
, the
gene set collection is filtered to contain only those sets implied
by the ids.
signature(object="character", idType="AnnotationIdentifier", setType="PfamCollection")
Construct a gene set collection by mapping all values in
object
to PfamIds
found in the PFAM
map
implied by idType
.
signature(object="character", idType="AnnotationIdentifier", setType="PrositeCollection")
Construct a gene set collection by mapping all values in
object
to ipi_ids
found in the PFAM
map
implied by idType
.
signature(object="character", idType="AnnotationIdentifier", setType="ChrlocCollection")
Construct a gene set collection by mapping all values in
object
to chromosome, strand, and position information
found in the map implied by idType
.
signature(object="ExpressionSet", idType="missing", setType="CollectionType")
,
signature(object="ExpressionSet", idType="missing", setType="CollectionIdType")
annotation
and
featureNames
of object
to identify elements for
CollectionType
gene sets (e.g., pathways for
KEGGCollection
, protein families for PfamCollection
)
implied by object
. The gene set
collection contains only those AnnotationIdentifiers
found
in featureNames(object)
; if setType
is a
CollectionIdType
and length(ids(setType))>0
, the
gene set collection is further filtered to contain only those sets
implied by the ids.
signature(object="ExpressionSet", idType="missing", setType="GOCollection")
annotation
and
featureNames
of object
to identify
GO
pathways implied by object
. The map between
featureNames
and GO
pathway identifiers is derived
from the GO2PROBE
table of the annotation
package of object
. The gene set collection contains only
those AnnotationIdentifiers
found in
featureNames(object)
. The evidenceCode
of
GOCollection
can be used to restrict the pathways seleted to
those with matching evidence codes.
signature(object="ExpressionSet", idType="missing", setType="PfamCollection")
Construct a gene set collection by mapping all values in
featureNames(object)
to PfamIds
found in the
PFAM
map implied by idType=AnnotationIdentifer(annotation(object))
.
signature(object="ExpressionSet", idType="missing", setType="PrositeCollection")
Construct a gene set collection by mapping all values in
featureNames(object)
to ipi_id
found in the
PFAM
map implied by idType=AnnotationIdentifer(annotation(object))
.
signature(object="ExpressionSet", idType="missing", setType="ChrlocCollection")
Construct a gene set collection by mapping all values in
featureNames(object)
to chromosome, strand, and position
information found in the CHRLOC
map implied by
idType=AnnotationIdentifer(annotation(object))
.
signature(object="missing", idType="AnnotationIdentifier", setType="GOCollection")
idType
. See the
signature(object="ExpressionSet", idType="missing",
setType="GOCollection")
method for details.
GeneSetCollection
-class
gs1 <- GeneSet(setName="set1", setIdentifier="101") gs2 <- GeneSet(setName="set2", setIdentifier="102") ## construct from indivdiual elements... gsc <- GeneSetCollection(gs1, gs2) ## or from a list gsc <- GeneSetCollection(list(gs1, gs2)) ## set names must be unique try(GeneSetCollection(gs1, gs1)) data(sample.ExpressionSet) gsc <- GeneSetCollection(sample.ExpressionSet[200:250], setType = GOCollection()) ## Not run: ## from KEGG identifiers, for example library(KEGG.db) lst <- head(as.list(KEGGEXTID2PATHID)) gsc <- GeneSetCollection(mapply(function(geneIds, keggId) { GeneSet(geneIds, geneIdType=EntrezIdentifier(), collectionType=KEGGCollection(keggId), setName=keggId) }, lst, names(lst))) ## End(Not run)